Multilayer OMIC Data in Medullary Thyroid Carcinoma Identifies the STAT3 Pathway as a Potential Therapeutic Target in <i>RET</i>^M918T Tumors.

Abstract

<b>Purpose:</b> Medullary thyroid carcinoma (MTC) is a rare disease with few genetic drivers, and the etiology specific to each known susceptibility mutation remains unknown. Exploiting multilayer genomic data, we focused our interest on the role of aberrant DNA methylation in MTC development.<b>Experimental Design:</b> We performed genome-wide DNA methylation profiling assessing more than 27,000 CpGs in the largest MTC series reported to date, comprising 48 molecularly characterized tumors. mRNA and miRNA expression data were available for 33 and 31 tumors, respectively. Two human MTC cell lines and 101 paraffin-embedded MTCs were used for validation.<b>Results:</b> The most distinctive methylome was observed for <i>RET</i>^M918T-related tumors. Integration of methylation data with mRNA and miRNA expression data identified genes negatively regulated by promoter methylation. These <i>in silico</i> findings were confirmed <i>in vitro</i> for <i>PLCB2, DKK4, MMP20</i>, and miR-10a, -30a, and -200c. The mutation-specific aberrant methylation of <i>PLCB2, DKK4</i>, and <i>MMP20</i> was validated in 25 independent MTCs by bisulfite pyrosequencing. The methylome and transcriptome data underscored JAK/Stat pathway involvement in <i>RET</i>^M918T MTCs. Immunostaining [immunohistochemistry (IHC)] for the active form of signaling effector STAT3 was performed in a series of 101 MTCs. As expected, positive IHC was associated with <i>RET</i>^M918T-bearing tumors (<i>P</i> < 0.02). Pharmacologic inhibition of STAT3 activity increased the sensitivity to vandetanib of the <i>RET</i>^M918T-positive MTC cell line, MZ-CRC-1.<b>Conclusions:</b> Multilayer OMIC data analysis uncovered methylation hallmarks in genetically defined MTCs and revealed JAK/Stat signaling effector STAT3 as a potential therapeutic target for the treatment of <i>RET</i>^M918T MTCs. <i>Clin Cancer Res; 23(5); 1334-45. ©2016 AACR</i>.